Workflow: qiime2 create phylogenetic tree
Fetched 2025-12-20 09:27:25 GMT
Verified with cwltool version 3.1.20221201130942
Generate a tree for phylogenetic diversity analyses from https://docs.qiime2.org/2018.4/tutorials/moving-pictures/
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- Inputs/Outputs
This workflow is Open Source and may be reused according to the terms of:
MIT License
Note that the tools invoked by the workflow may have separate licenses.
Inputs
| ID | Type | Title | Doc |
|---|---|---|---|
| rooted_tree_filename | String | ||
| unrooted_tree_filename | String | ||
| representative_sequences | File | ||
| aligned_rep_seqs_filename | String | ||
| masked_aligned_rep_seqs_filename | String |
Steps
| ID | Runs | Label | Doc |
|---|---|---|---|
| root_tree |
../tools/qiime2/phylogeny-midpoint-root.cwl
(CommandLineTool)
|
qiime2: Midpoint root an unrooted phylogenetic tree | |
| create_tree_from_alignment |
../tools/qiime2/phylogeny-fasttree.cwl
(CommandLineTool)
|
qiime2: Construct a phylogenetic tree with FastTree | |
| mask_representative_sequences |
../tools/qiime2/alignment-mask.cwl
(CommandLineTool)
|
qiime2: Mask unconserved and highly gapped columns from an alignment | |
| align_representative_sequences |
../tools/qiime2/alignment-mafft.cwl
(CommandLineTool)
|
qiime2: Perform de novo multiple sequence alignment using MAFFT |
Outputs
| ID | Type | Label | Doc |
|---|---|---|---|
| rooted_tree | File | ||
| unrooted_tree | File | ||
| masked_representative_sequences | File | ||
| aligned_representative_sequences | File |
Permalink:
https://w3id.org/cwl/view/git/a6a7d5bd034f8ccf01b809bc9f5ecf87e5c5652c/subworkflows/qiime2-05-phylogeny.cwl
